gaggle 1.41.0
Christopher Bare
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gaggle | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gaggle_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaggle/DESCRIPTION’ ... OK
* this is package ‘gaggle’ version ‘1.41.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gaggle’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘RUnit’ ‘rJava’
Please remove these calls from your code.
Packages in Depends field not imported from:
‘RUnit’ ‘rJava’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘gaggle/R/gaggle.R’:
.onLoad calls:
require("rJava")
cat(paste("\nonLoad -- libname:", libname, "pkgname:", pkgname, "\n"))
cat("path to jar:", fullPathToGaggleJar, "\n")
cat(" script: ", .scriptVersion(), "\n")
cat(" os version: ", .jcall("java/lang/System", "S", "getProperty", "os.name"), "\n")
cat(" jvm version: ", jvmVersion, "\n")
cat("\n You are using the wrong version of Java.\n", " Please see http://gaggle.systemsbiology.org/docs/html/java\n\n")
Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in '?.onAttach'.
onLoad -- libname: /Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck pkgname: gaggle
path to jar: /Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Mac OS X
jvm version: 1.6.0_65
.broadcastAssociativeArray: no visible binding for global variable
‘goose’
.broadcastEnvironment: no visible binding for global variable ‘goose’
.broadcastGraph: no visible binding for global variable ‘goose’
.pkgVersion: no visible global function definition for ‘sessionInfo’
broadcast: no visible binding for global variable ‘goose’
connectToGaggle: no visible binding for global variable ‘goose’
disconnectFromGaggle: no visible binding for global variable ‘goose’
gaggleInit: no visible binding for '<<-' assignment to ‘goose’
gaggleInit: no visible binding for '<<-' assignment to ‘targetGoose’
gaggleInit: no visible binding for global variable ‘goose’
geese: no visible binding for global variable ‘goose’
getCluster: no visible binding for global variable ‘goose’
getMatrix: no visible binding for global variable ‘goose’
getNameList: no visible binding for global variable ‘goose’
getNetwork: no visible binding for global variable ‘goose’
getSpecies: no visible binding for global variable ‘goose’
getTargetGoose: no visible binding for global variable ‘goose’
getTuple: no visible binding for global variable ‘goose’
getTupleAsList: no visible binding for global variable ‘goose’
hideGoose: no visible binding for global variable ‘goose’
setSpecies: no visible binding for global variable ‘goose’
setTargetGoose: no visible binding for '<<-' assignment to
‘targetGoose’
setTargetGoose: no visible binding for global variable ‘goose’
showGoose: no visible binding for global variable ‘goose’
testGagglePackage: no visible global function definition for
‘test.gaggle’
Undefined global functions or variables:
goose sessionInfo test.gaggle
Consider adding
importFrom("utils", "sessionInfo")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: connectToGaggle.Rd:9-10: Dropping empty section \arguments
prepare_Rd: disconnectFromGaggle.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getCluster.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getNameList.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getTuple.Rd:6-7: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck/00check.log’
for details.
* installing *source* package ‘gaggle’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
onLoad -- libname: /Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck pkgname: gaggle
path to jar: /Users/biocbuild/bbs-3.4-bioc/meat/gaggle.Rcheck/gaggle/jars/gaggleRShell.jar
script: gaggle.R $Revision: 4499 $ $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $
os version: Mac OS X
jvm version: 1.6.0_65
* DONE (gaggle)